(v1.6.0.9041) filter_ab_class() fix

R/filter_ab_class.R

@@ -125,11 +125,11 @@ filter_ab_class <- function(x,
                          group %like% ab_class | 
                            atc_group1 %like% ab_class | 
                            atc_group2 %like% ab_class)
-  ab_group <- find_ab_group(ab_class)
-  if (ab_group == "") {
+  if (nrow(ab_reference) == 0) {
     message_("Unknown antimicrobial class '", ab_class.bak, "', data left unchanged.")
     return(x.bak)
   }
+  ab_group <- find_ab_group(ab_class.bak)
   # get the columns with a group names in the chosen ab class
   agents <- ab_in_data[names(ab_in_data) %in% ab_reference$ab]
   if (length(agents) == 0) {

R/first_isolate.R

@@ -435,7 +435,7 @@ first_isolate <- function(x = NULL,
   if (length(c(row.start:row.end)) == pm_n_distinct(x[c(row.start:row.end), col_mo, drop = TRUE])) {
     if (info == TRUE) {
       message_("=> Found ", font_bold(paste(length(c(row.start:row.end)), "first isolates")),
-               ", as all isolates were different microorganisms",
+               ", as all isolates were different microbial species",
                add_fn = font_black,
                as_note = FALSE)
     }

R/mdro.R

@@ -306,7 +306,7 @@ mdro <- function(x = NULL,
   }
   if (is.null(col_mo) & guideline$code == "tb") {
     message_("No column found as input for `col_mo`, ",
-             font_bold(paste0("assuming all records contain", font_italic("Mycobacterium tuberculosis"), ".")))
+             font_bold(paste0("assuming all rows contain ", font_italic("Mycobacterium tuberculosis"), ".")))
     x$mo <- as.mo("Mycobacterium tuberculosis") # consider overkill at all times: MO_lookup[which(MO_lookup$fullname == "Mycobacterium tuberculosis"), "mo", drop = TRUE]
     col_mo <- "mo"
   }